Mostly mostly of the Gyms and Elite 4 don't use Mega Evolutions
Here's what they could have used (Perhaps in re-match even)
Viola: Mega Pinsir or Mega Beedrill
Grant: Mega Aerodactyl
Korrina: She has Mega Lucario
Ramos: Mega Venusaur
Clemont: Mega Ampharos
Valerie: Mega Mawile
Olympia: Mega Alakazam
Wulfric: Mega Abomasnow
Elite 4
Malva: Mega Houndoom
Wikstrom: Mega Steelix
Siebold: Mega Blastoise
Drasna: Mega Altaria
I've got my own issue; trying to find Moltres 10 times so it can go back to the Sea Spirit Den. I hate random it flies in Kalos and trying to find out how to corner it.
Oh They definitely could have also given them Megas. Even if you limit them to just the Megas available in X&Y they had enough options to give every gym leader and elite 4 a mega if they wanted them to.
Viola-Mega Heracross or Mega Pinsir (either works)
Grant- Mega Aerodactyl or Mega Tyranitar (either works)
Korrina- already established as Mega Lucario
Ramos- As you said Mega Venasaur
Clemont- Mega Manectric
Valerie-Mega Mawile
Olympia- Mega Alakazam
Wulfric- Mega Abomasnow
Malva-Mega Houndoom, Blaziken or Charizard Y(I personally prefer Houndoom)
Wikstrom- Mega Scizor or Mega Aggron ( I personally prefer Scizor)
Drasna- Mega Ampharos or Charizard X (I personally prefer Ampharos)
Siebold- Mega Blastoise (would be Gyarados as an option but that's used by Lysandre but I prefer Blastoise anyway)
Then again the rematches in X and Y really limited the number of Pokemon. I'd have liked to have seen gym rematches with full teams at least.